Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01020933.1 Corchorus olitorius cultivar O-4 contig20966, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 23618
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35


Found at i:4885 original size:15 final size:15

Alignment explanation


    Indices: 4867--4908  Score: 57
    Period size: 15  Copynumber: 2.8  Consensus size: 15

       4857 TGGAAACTTC

                           
       4867 TTCGATTGTCTCAGA
          1 TTCGATTGTCTCAGA

                        *  
       4882 TTCGATTGTCTCGGA
          1 TTCGATTGTCTCAGA

              *    *    
       4897 TTTGATTTTCTC
          1 TTCGATTGTCTC

       4909 TTCCTTCATG


Statistics
Matches: 24,  Mismatches: 3, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   24  1.00

ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48


Consensus pattern (15 bp):   
TTCGATTGTCTCAGA

Found at i:11436 original size:76 final size:76

Alignment explanation


    Indices: 11304--11455  Score: 173
    Period size: 76  Copynumber: 2.0  Consensus size: 76

      11294 TACCGAGCCA

                        *      *    *                  *       *             
      11304 TGACACAGCCCATCTGGGTGATCAGGCGAAACACATGGGTCTTCAGACAAAGCATGTGGGCACCC
          1 TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGGTCTTAAGACAAACCATGTGGGCACCC

                       
      11369 AGCTGGAGTCG
         66 AGCTGGAGTCG

                  *             *                           *             ** 
      11380 TGACACTGCCCACCTGGGTCCTCAAGC-AAACCACATGGGTGCTTAAGGC-AACCATGTGGGTGC
          1 TGACACAGCCCACCTGGGTCATCAAGCGAAA-CACATGGGT-CTTAAGACAAACCATGTGGGCAC

                *        
      11443 CCAGGTGGAGTCG
         64 CCAGCTGGAGTCG

      11456 GGGCCCTTGT


Statistics
Matches: 63,  Mismatches: 11, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  75    3  0.05
  76   54  0.86
  77    6  0.10

ACGTcount: A:0.24, C:0.28, G:0.30, T:0.18


Consensus pattern (76 bp):   
TGACACAGCCCACCTGGGTCATCAAGCGAAACACATGGGTCTTAAGACAAACCATGTGGGCACCC
AGCTGGAGTCG

Found at i:15260 original size:26 final size:26

Alignment explanation


    Indices: 15230--15279  Score: 100
    Period size: 26  Copynumber: 1.9  Consensus size: 26

      15220 GTTGCATATT

                                      
      15230 AGCAATAATATTTGAAGAGGGTAACA
          1 AGCAATAATATTTGAAGAGGGTAACA

                                    
      15256 AGCAATAATATTTGAAGAGGGTAA
          1 AGCAATAATATTTGAAGAGGGTAA

      15280 AAAATTTGGA


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  26   24  1.00

ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24


Consensus pattern (26 bp):   
AGCAATAATATTTGAAGAGGGTAACA

Found at i:17071 original size:19 final size:18

Alignment explanation


    Indices: 17047--17082  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

      17037 TGAAGATTTA

                               
      17047 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
      17066 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

      17083 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT
Done.